iscream

iscream queries compressed and uncompressed BED files containing ranged genomic data and returns results as data frames, GenomicRanges objects, matrices, or SummarizedExperiment objects, with specialized support for methylation data import.

Key Features:

• BED File Querying: Queries ranged genomic data from BED files regardless of compression status.
• Multiple Output Formats: Returns parsed records or summary statistics as data frames or GenomicRanges objects, and matrices as matrix, GenomicRanges, or SummarizedExperiment objects.
• Methylation Data Support: Provides specialized functionality for importing methylation data from BED files.

Scientific Applications:

• Genomic Data Extraction: Retrieves ranged genomic data from BED files for downstream analysis in R/Bioconductor workflows.
• Methylation Analysis: Imports and processes methylation data stored in BED format for epigenetic studies.

Methodology:

The tool queries BED files and returns data in multiple Bioconductor object classes including GenomicRanges and SummarizedExperiment.